From 965f0cfe3e8498a3e4c050ac6d6be1a90edf1dbb Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 17 Feb 2021 10:57:48 +0100
Subject: [PATCH] fixed bad subspecies names
---
bacdive2alvisnlp.xslt | 14 --------------
dsmz-match.plan | 6 +++---
2 files changed, 3 insertions(+), 17 deletions(-)
diff --git a/bacdive2alvisnlp.xslt b/bacdive2alvisnlp.xslt
index 5a3fe2f..bdb35ea 100644
--- a/bacdive2alvisnlp.xslt
+++ b/bacdive2alvisnlp.xslt
@@ -16,20 +16,6 @@
<xsl:template match="taxonomy_name/strains/list-item">
<a:section name="species" xpath-contents="species"/>
- <xsl:variable name="complete">
- <xsl:choose>
- <xsl:when test="subspecies_epithet != ''">
- <xsl:value-of select="concat(species, ' ', subspecies_epithet)"/>
- </xsl:when>
- <xsl:when test="species_epithet != ''">
- <xsl:value-of select="species"/>
- </xsl:when>
- <xsl:otherwise>
- <xsl:value-of select="genus"/>
- </xsl:otherwise>
- </xsl:choose>
- </xsl:variable>
- <a:section name="complete" xpath-contents="$complete"/>
<a:section name="full_scientific_name" xpath-contents="normalize-space(full_scientific_name)"/>
<a:section name="designation" xpath-contents="designation"/>
</xsl:template>
diff --git a/dsmz-match.plan b/dsmz-match.plan
index c46b7a9..0d02a85 100644
--- a/dsmz-match.plan
+++ b/dsmz-match.plan
@@ -27,7 +27,7 @@
<strain-name class="Action">
<target>documents.sections:strain-number</target>
- <action>document.new:section:strain-name(sections:complete.contents ^ " " ^ target.contents)</action>
+ <action>document.new:section:strain-name(sections:species.contents ^ " " ^ target.contents)</action>
<createSections/>
</strain-name>
@@ -44,7 +44,7 @@
<lines>documents.sections[@taxid]</lines>
<columns>
document.@id,
- document.sections:complete.contents,
+ document.sections:species.contents,
document.sections:full_scientific_name.contents,
@name,
contents,
@@ -54,7 +54,7 @@
</columns>
<headers>
"ID",
- "COMPLETE NAME",
+ "SPECIES NAME",
"FULL NAME",
"FIELD",
"NAME",
--
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